[Obo-cell-type] Annotations to cell types (using OBO-Cell)

[Pankaj Jaiswal]

Sue, its a good idea to establish  Xrefs between CT and PO.

Just a preliminary look at both the CT and PO for plant cell and its 
instances. Seems to be that there are more cell types listed in PO 
(almost double). Also the free text definitions are not consistent with 
those from PO. So I am not sure what is the source of the plant cell 
types in CT.

To avoid the inconsistencies, I suggest that the primary source of all 
the plant cell types in CT should be PO and not the other way round. If 
in case the CT needs new Plant cell types then a request be forwarded to 
PO. CT managers can later using an automated way collect/update it by 
pulling the plant cell type terms from PO. Alternatively we can also 
generate a mapping file PO2CT and use it for QC and consistency across 
both. Based on your suggestions I can ask Shuly to generate a mapping 
and add the related ontology DBXref to the PO terms.

BTW one more suggestion, is it possible to add the 'subset: plant' or a 
namespace:plant to quickly identify which terms belong to the plant cell 
types. The same is suggested for cell types from other organisms as well.

Any ideas?

Pankaj

Sue Rhee wrote:
> Chris,
> 
> The Plant Ontology has a number of cell types under its Plant Structure 
> branch and I think (though someone should confirm) that the Cell Type 
> ontology's plant cell type terms have PO IDs as secondary IDs. Actually 
> I think that this should be made bidirectional but am not sure if the PO 
> terms have CT IDs as secondary IDs. In any case, there are 264 
> annotations to terms under plant cell, which are downloadable from the 
> PO website (www.plantontology.org).
> 
> Sue
> 
> Chris Mungall wrote:
>> Is anyone aware of downloadable annotations to CL IDs? I know that  
>> MGI provide cell type localisation info as qualifiers to their GO  
>> annotations; this will be available through AmiGO sometime this year.
>>
>> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many of  
>> which are described as qualities borne by types of cell (eg  
>> spermatocyte lacks asters)
>>
>> EVOC provides associations to dbEST libraries.
>>
>> Any others?
>>
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> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683